Surface Exposed Residues

Here is how to select surface exposed residues that are hydrophobic.

Use ​measure sasa to define an "area" attribute of residues, then assign residue hydrophobicities from a file with the ​defattr command, and then use a single ​select command to intersect these two attributes.

In the ​defattr example files I already happened to include a file kdHydrophobicity.txt to assign Kyte-Doolittle hydrophobity, as well as for several other hydrophobicity scales. Just download whichever one(s) you want.

The commands could be something like:

open 6g2j
measure sasa protein
defattr ~/Desktop/kdHydrophobicity.txt
select ::area>25 & ::kdHydrophobicity>0.0
surface protein enclose protein
color sel magenta

... which looks like this ...

... in pretty good agreement with MLP coloring, e.g.

mlp surfaces #1.3

In the select command you may want to experiment with the surface-area and hydrophobicity cutoffs, as well as which hydrophobicity scale you use. I didn't try a lot of values for surface-area cutoff, but here is with all residues with values >25 colored red, reasonable at least as a first approximation:

Elaine Meng